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Issue Type:
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![Bug]() Bug
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Affects Versions:
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JRuby 1.7.0.pre1, JRuby 1.6.7 |
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Assignee:
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Thomas E Enebo
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Created:
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09/Jul/12 3:42 PM
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Description:
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As indicated in https://github.com/csw/bioruby-maf/issues/31, a particular subset of unit tests involving the @sequence_filter instance variable of Bio::MAF::Parser (see lib/bio/maf/parser.rb) will pass when run by themselves, but fail when certain other unit tests (tagged with :bug in spec/bio/maf/parser_spec.rb) are also executed. If the instance variable is explicitly set to nil in the constructor, or any of the three #fetch_blocks unit tests tagged with :bug are not executed, or the variable is read with @sequence_filter rather than calling the Parser#sequence_filter accessor method, the bug disappears. I have not been able to narrow down the bug any further or come up with a good explanation of this; I suspect some sort of compiler bug.
I have come up with a workaround, but this is clearly a bug of some sort; MRI works fine with the same code.
To reproduce:
git clone https://github.com/csw/bioruby-maf.git
cd bioruby-maf
git checkout jruby-sequence-filter-bug
rvm use jruby-head [or equivalent]
bundle install
rspec -e sequence_filter
[passes]
rspec -t bug
[fails]
Let me know if I can help refine this any further.
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Environment:
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Mac OS X 10.7.4, Java 64-bit server VM 1.7.0_04. Reproduced under versions above as well as commit 903a934 from July 6.
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Project:
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JRuby
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Priority:
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![Major]() Major
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Reporter:
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Clayton Wheeler
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